Dear Bioconductor Helpers,
I have used Bioconductor to analyze Affy chips only, but recently I have to
do some analysis for Agilent array. Each array has the two chips with the
same sample but the dye swapped (I just made it clear as I saw most of the
literature on such arrays with 4 chips).

Can any one help me how to:
1 - Import data in Bioconductor? (I mean what is the equivalent of .cel
files here - if there is any? I have a few .xml .csv, .txt and .shp files -
I am clueless which ones to use and how should I use)
2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter seems
to be for the 4 chip Agilent array) related to Agilent arrays.
     Can anyone point out a good article to read on - how to (completely)
analyze such Agilent Arrays - importing, "cleaning up" and analyzing data?
3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma to
analyze this data after I am done importing data correctly.

I am sorry if I used Agilent array/chip in a wrong way, my knowledge is very
limited in this area. I have only analyzed Affy arrays until now.

Any help will be appreciated.

Thanks,
S.

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